RotamerMolecule

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KEYWORD

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CHANGES LOG

GOALS

USAGE

Class Summary

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KEYWORD

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AUTHORS

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CHANGES LOG

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GOALS

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USAGE

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RotamerMolecule(const ChemMolecule& origMolecule);

    RotamerMolecule(const ChemMolecule& origMolecule);

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~RotamerMolecule();

    virtual ~RotamerMolecule();

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int buildAllRotamers(const RotamerLibrary& rotamerLib, unsigned short maxNumOfRotamers );

    int buildAllRotamers(const RotamerLibrary& rotamerLib, unsigned short maxNumOfRotamers = 44);    

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int buildSurfaceRotamers(const RotamerLibrary& rotamerLib, string chainIds, bool extraForChi1 , bool extraForChi2 , float nativeFavorFactor, unsigned short maxNumOfRotamers);

    int buildSurfaceRotamers(const RotamerLibrary& rotamerLib, string chainIds, bool extraForChi1 , bool extraForChi2 , 
                                          float nativeFavorFactor, unsigned short maxNumOfRotamers);

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int buildResiduesRotamers(const RotamerLibrary& rotamerLib, const vector< bool>& residuesForBuild);

    int buildResiduesRotamers(const RotamerLibrary& rotamerLib, const vector< bool>& residuesForBuild);

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int buildResiduesRotamers(const RotamerLibrary& rotamerLib, const vector< bool>& residuesForBuild, const vector< bool>& matchedResidues);

    int buildResiduesRotamers(const RotamerLibrary& rotamerLib, const vector< bool>& residuesForBuild, const vector< bool>& matchedResidues);

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int findInterfaceResidues(const RotamerMolecule& partner, const RigidTrans3& rigidTrans3, float interfaceThr, vector< bool>& interfaceResidues, vector< bool>& partnerInterfaceResidues);

    int findInterfaceResidues(const RotamerMolecule& partner, const RigidTrans3& rigidTrans3, float interfaceThr,
                              vector< bool>& interfaceResidues, vector< bool>& partnerInterfaceResidues);

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void setFlexibleResidues( const vector< bool>& flexibleResidues);

    void setFlexibleResidues(/*const RotamerLibrary& rotamerLib,*/ const vector< bool>& flexibleResidues);

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vector< unsigned int> getSASAOfResidues(string chainIds);

    vector< unsigned int> getSASAOfResidues(string chainIds);

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vector< unsigned int> getResiduesSurfaceFrequencies(const string chainIds) const ;

    vector< unsigned int> getResiduesSurfaceFrequencies(const string chainIds) const ;

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Molecule< Atom> buildMoleculeWithTrimedFlexResidues() const;

    Molecule< Atom> buildMoleculeWithTrimedFlexResidues() const;

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Molecule< Atom> buildCurrentMolecule() const;

    Molecule< Atom> buildCurrentMolecule() const;

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Molecule< Atom> buildConformersMolecule() const;

    Molecule< Atom> buildConformersMolecule() const;

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const vector< const RotamerAtom *>& getAllAtoms() const;

    const vector< const RotamerAtom *>& getAllAtoms() const;

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const vector< const RotamerAtom *>& getCurrentAtoms() const;

    const vector< const RotamerAtom *>& getCurrentAtoms() const; 

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void setNativeState();

    void setNativeState();

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unsigned int getNumOfAllAtoms() const ;

    inline unsigned int getNumOfAllAtoms() const                                              ;

Function is currently defined inline.

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unsigned int getNumOfAllConformers() const ;

    inline unsigned int getNumOfAllConformers() const                                                   ;

Function is currently defined inline.

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void currentStateChanged() ;

    inline void currentStateChanged()
                                                  
;

Function is currently defined inline.

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void chooseNearestNativeRotamers();

    void chooseNearestNativeRotamers();

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void chooseRandomRotamers();

    void chooseRandomRotamers();

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unsigned short generateNextConformerSequence() const ;

    unsigned short generateNextConformerSequence() const                                                                                           ;

Function is currently defined inline.

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unsigned short generateNextBackboneSequence() const ;

    unsigned short generateNextBackboneSequence() const                                                                                          ;

Function is currently defined inline.

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unsigned int generateNextAtomSequence() const ;

    unsigned int generateNextAtomSequence() const                                                                                      ;

Function is currently defined inline.

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Vector3 operator()(unsigned int atomIndex) const;

for templates support (HashInterface< const RotamerMolecule>,MolIntersection< const RotamerMolecule>)

    Vector3 operator()(unsigned int atomIndex) const;

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const RotamerAtom& operator[](unsigned int atomIndex) const;

    const RotamerAtom& operator[](unsigned int atomIndex) const;

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unsigned int size() const;

    unsigned int size() const;

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unsigned short getNumOfResidues() const ;

    unsigned short getNumOfResidues() const                                        ;

Function is currently defined inline.

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const RotamerResidue& getResidue(unsigned short residueSeq) const ;

    const RotamerResidue& getResidue(unsigned short residueSeq) const                                              ;

Function is currently defined inline.

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RotamerResidue& getResidue(unsigned short residueSeq) ;

    RotamerResidue& getResidue(unsigned short residueSeq)                                             ;

Function is currently defined inline.

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const RotamerResidue& getResidue(const char chainID, const string residueSeqInPDB) const ;

    const RotamerResidue& getResidue(const char chainID, const string residueSeqInPDB) const ;

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unsigned short getMoleculeSequence() const ;

    unsigned short getMoleculeSequence() const                                         
;

Function is currently defined inline.

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void printDihedralAngles(ostream& s) const;

    void printDihedralAngles(ostream& s) const;

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void printResidueConformers(ostream& s, const char chainID, const string residueSeqInPDB) const;

    void printResidueConformers(ostream& s, const char chainID, const string residueSeqInPDB) const;

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void printBonds(ostream& s) const;

    void printBonds(ostream& s) const;

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friend ostream& operator<<(ostream& s, const RotamerMolecule& m);

    friend ostream& operator<<(ostream& s, const RotamerMolecule& m);

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unsigned int AMPLfile2CurrentState(istream& s, unsigned int& numOfNativeConformers, unsigned int& numOfMovableConformers, unsigned int AMPLConformersStartCounter );

    unsigned int AMPLfile2CurrentState(istream& s, /*const vector< bool>& chosenResidues, */
                                       unsigned int& numOfNativeConformers, unsigned int& numOfMovableConformers, 
                                       unsigned int AMPLConformersStartCounter = 0);

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unsigned int AMPLfile2CurrentState(string fileName, unsigned int& numOfNativeConformers, unsigned int& numOfMovableConformers, unsigned int AMPLConformersStartCounter );

    unsigned int AMPLfile2CurrentState(string fileName, /*const vector<bool>& chosenResidues, */
                                       unsigned int& numOfNativeConformers, unsigned int& numOfMovableConformers, 
                                       unsigned int AMPLConformersStartCounter = 0);

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const RotamerResidue * findResidue(const char chainID, const string residueSeqInPDB) const;

    const RotamerResidue * findResidue(const char chainID, const string residueSeqInPDB) const;    

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All Members

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Ancestors

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Descendants

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